They believe synths have free will. That does not mean they respect all choices that synths make. Just like acknowledging that humans have free will does not mean that you need to be nice to humans that decide to become raiders.
The Railroad believes the Institute to be an Evil organization, just like the BoS. For all of the same reasons as the Minutemen do but they think that the synths that escape deserve to be treated like refugees and not destroyed because of what they are.
I guess Bethesda needs to simplify their writing again is the take away from the forums.